Transmissible spongiform encephalopathies (TSEs or prion diseases) are a group of rare neurodegenerative diseases which include sporadic Creutzfeldt-Jakob disease (sCJD) in humans, scrapie in sheep, bovine spongiform encephalopathy (BSE), and chronic wasting disease (CWD) in mule deer and elk. Prions can cross species barriers. The fact that BSE has infected humans in Great Britain and concerns that CWD may act similarly in the US underscores the importance of understanding prion pathogenesis and developing effective therapeutics. The infectious agent of prion diseases is called a prion and is largely composed of an abnormally refolded, protease resistant form (PrPSc) of the normal, protease-sensitive prion protein, PrPC. Susceptibility to infection can be influenced by amino acid homology between PrPC and PrPSc while differences in structure between PrPSc molecules are believed to encode strain phenotypes. My laboratory addresses many different aspects of prion diseases at both the molecular and pathogenic level. In particular, my studies focus on: 1) identifying the earliest events which occur during prion infection, 2) defining the molecular pathways involved in prion-associated neurodegeneration, 3) determining the molecular basis of prion strains, 4) determining how PrPC sequence and post-translational modifications influence PrPSc formation and disease phenotype and, 5) development of effective prion therapeutics. Although there is an increasing body of work suggesting that mitochondrial dysfunction is important in several neurodegenerative protein misfolding diseases such as Alzheimers disease (AD) and Parkinsons disease (PD), the role of mitochondria in prion disease is poorly understood. We recently published data showing that PrPC is present in brain mitochondria from healthy wild-type and transgenic mice Faris et al., Sci. Rep. 7: 41556 (2017), Annual Report 2017. We have also found evidence that mitochondria may be impaired in mice overexpressing PrPC. Faris et al., J. Virol. 91: e00524-17 (2017), Annual Report 2017. Our data suggest that, as has been proposed for other proteins associated with neurodegenerative disorders, PrPC may play a role in mitochondrial function. In 2018, we continued studies looking at prion disease progression and mitochondrial dysfunction in mice with known mitochondrial defects. We also initiated studies aimed at identifying how PrPC expression level, post-translational modifications, and structure effect mitochondrial viability. These latter studies are in collaboration with Dr. Catharine Bosio's laboratory which has a Seahorse XF Analyzer to measure mitochondrial respiration and viability. Amino acid mismatches between PrPC and PrPSc influence the rate at which PrPSc forms and heterozygosity at key residues has the potential to significantly slow or even prevent disease transmission J Gen Virol 93: 2749-2756 (2012). In human PrPC, methionine/valine heterozygosity at codon 129 influences prion transmission and is a known resistance factor to sCJD ACTA Neuropathol 130: 159-170 (2015). It is possible that the ratio of PrPSc with methionine at codon 129 (PrPSc-M129) to PrPSc with valine at codon 129 (PrPSc-V129) determines the efficient transmission of prions in heterozygous cases of CJD. In 2018, we completed a long-term in vivo experiment to test the efficiency of transmission of codon 129 heterozygous cases of CJD. We had previously determined the ratio of PrPSc-M129 to PrPSc-V129 in these cases (Moore et al. PLoS Pathog. 12: e1005416 (2016), Annual Report 2016). We are currently in the process of finishing the biochemical characterization of PrPSc in these mice and expect to publish the results in the coming year. These experiments will determine the influence of the PrPSc allotype ratio on prion disease tempo and transmission and will provide important insights into the mechanisms underlying CJD progression in humans. In 2018, we also completed an initial study looking at the fate of host PrPC following intracranial prion inoculation. These studies were designed to provide critical information about the events that occur during the first few hours following exposure to prions. A manuscript describing this study has been completed and will be submitted soon. The prion agent is notoriously difficult to inactivate with the routine sterilization protocols used in hospitals where iatrogenic transmission of CJD is an ongoing concern. The extreme resistance of prions to inactivation and their ability to persist in the environment for decades thus remains a significant public health issue. Similar concerns apply to the laboratory setting where it is often necessary to analyze prion samples using advanced analytical techniques that are frequently only available outside of biosafety level 2 (BSL-2) containment, the minimum biosafety level required for studying infectious prions. However, the remarkable resistance of prions to inactivation can make it difficult to produce and analyze prion samples free of infectivity that still retain sufficient sample integrity for research purposes. In 2018, we published a study demonstrating that a straightforward denaturation and in-gel protease digestion protocol used to prepare prion-infected samples for mass spectroscopy leads to the loss of at least 7 logs of prion infectivity. The final product failed to transmit prion disease in vivo yet remained suitable for mass spectrometry-based protein identifications. Our results show that prion-infected samples processed for mass spectrometry can be suitable for analysis without an absolute requirement for BSL-2 containment. They will be of use to regulators, biosafety specialists, and researchers tasked with determining whether or not prion-infected samples can be safely analyzed outside of BSL-2 containment.